最近需要盡可能的下載細(xì)菌基因組挣郭，ncbi ftp站點(diǎn)（ftp://ftp.ncbi.nlm.nih.gov/genomes）里面"all"這個(gè)目錄可以下載，不過"all"目錄還有古細(xì)菌之類的哈倔矾。如果只想取Refseq或genbank數(shù)據(jù)庫其一，可以通過以下方式：

#下載Refseq/genbank數(shù)據(jù)庫中的細(xì)菌基因組數(shù)據(jù)
#截止20190106，有140681條基因組數(shù)據(jù)
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt
#文件第12列是拼接狀態(tài)（Complete Genome/Scaffold/contig），第20列是ftp路徑载慈，下面是下載組裝完整的基因組信息
awk -F "\t" '$12=="Complete Genome" && $11=="latest"{print $20}' assembly_summary.txt > ftpdirpaths
awk 'BEGIN{FS=OFS="/";filesuffix="genomic.gbff.gz"}{ftpdir=$0;asm=$10;file=asm"_"filesuffix;print ftpdir,file}' ftpdirpaths > ftpfilepaths
cut -d / -f 11 ftpfilepaths | paste - ftpfilepaths  | while read a b;do echo "wget -c -nd -r -np -k -L -p -nd -P genbank $b && gzip -d genbank/$a";done >run.download.sh
#腳本只下載了gbff文件，當(dāng)然珍手，如果想要gff,fna,faa通過小腳本轉(zhuǎn)就可以了，或者加上“-A faa.gz,fna.gz,gff.gz,gpff.gz”

真的超級(jí)占存儲(chǔ)空間辞做，我只下載gbff文件琳要，需要其他格式的文件再簡單格式轉(zhuǎn)化就可以了。同時(shí)秤茅，下載一批立馬處理一批稚补。
Refseq和genbank的區(qū)別
Refseq下載的是GCF開頭的文件，而genbank下載的是GCA開頭的文件框喳。

具體看這里：https://zhuanlan.zhihu.com/p/20749737

GenBank是核苷酸數(shù)據(jù)庫课幕，RefSeq是基因數(shù)據(jù)庫 ，具體哪個(gè)更全五垮？互為補(bǔ)充乍惊，以前做分析的時(shí)候發(fā)現(xiàn)有些細(xì)菌基因組在GenBank里面沒有在RefSeq有，還有可能兩個(gè)數(shù)據(jù)庫里面某個(gè)基因組只有一個(gè)fna文件沒有注釋放仗，這種情況如果遇到自己動(dòng)手用prokka十分鐘就能解決润绎。

生信小腳本收藏癖，有時(shí)遇到比較實(shí)用的腳本會(huì)存下來放在自己環(huán)境變量bin里面诞挨，積累會(huì)使以后的分析變得更加高效

附上兩個(gè)網(wǎng)上看到好用的腳本

1.GenBank轉(zhuǎn)faa格式

#!/usr/bin/env perl
# This program reads gbk files and extracts all amino acid sequences from the
# /translation fields into a FASTA file. The FASTA header contains a sequential
# number followed by the taxon id, which is extracted from the
# /db_xref="taxon:<ID>" field. Only letters in the 20 letter amino acid
# alphabet are retained in the FASTA file.
#
# author: Peter Menzel
#
# This file is part of Kaiju, Copyright 2015-2017 Peter Menzel and Anders Krogh
# Kaiju is licensed under the GPLv3, see the file LICENSE.
#

use strict;
use warnings;
use IO::Uncompress::AnyUncompress qw(anyuncompress $AnyUncompressError) ;

my $t = 0;
my $taxid;
my $protein_id;

if(!defined $ARGV[1]) { die "Usage: $0 infile.gbk outfile.faa"; }
open(OUT,">",$ARGV[1]) or die "Could not open file $ARGV[1] for writing.";
my $in_fh = new IO::Uncompress::AnyUncompress $ARGV[0] or die "Opening input file failed: $AnyUncompressError\n";

while(<$in_fh>) {
    chomp;
    if(m,/db_xref="taxon:(\d+)",) {
        $taxid = $1;
    }
    elsif(m,/protein_id="([^"]+)",) {
        $protein_id=$1;
    }
    elsif(m,\s+/translation="([^"]+)",)  {  
        if(!defined($taxid)) { die "No taxon id found in gbk file $ARGV\n";}
        print OUT ">$protein_id\_$taxid\n";
        my $seq = $1;
        $seq =~ tr/BZ/DE/;  # a.a. alphabet specifies `B' matches `N' or `D', and `Z' matches `Q' or `E.', here we use substitution with higher score
        $seq =~ s/[^ARNDCQEGHILKMFPSTWYV]//gi;
        print OUT "$seq\n";
    }
    elsif(m,\s+/translation="([^"]+)$,) {
        if(!defined($taxid)) { die "No taxon id found in gbk file $ARGV\n";}
        print OUT ">$protein_id\_$taxid\n";
        $t = 1;
        my $seq = $1;
        $seq =~ tr/BZ/DE/;
        $seq =~ s/[^ARNDCQEGHILKMFPSTWYV]//gi;
        print OUT "$seq\n";
    }
    elsif($t) {
        if(m,",) { 
            tr/BZ/DE/;
            s/[^ARNDCQEGHILKMFPSTWYV]//gi;
            print OUT $_,"\n";   
            $t = 0;
        }
        else { 
            tr/BZ/DE/;
            s/[^ARNDCQEGHILKMFPSTWYV]//gi;
            print OUT $_,"\n";   
        }
    }
}
close($in_fh);
close(OUT);

2.Genbank轉(zhuǎn)fna格式

#!/usr/bin/env python

import sys
from Bio import SeqIO

if len(sys.argv) < 3:
    print('USAGE: gbk2fna GBK FNA')
    sys.exit(65)

SeqIO.write(SeqIO.parse(sys.argv[1], 'genbank'), sys.argv[2], 'fasta')